Glossary
of Paleontological, Geological and Biological terms

abyssal
plain: Large area of extremely flat ocean floor lying near
a continent and generally over 4 km in depth.

acanthodians:
Now extinct, earliest group of fish with jaws, ranging
from
the Silurian to the Permian.

acritarchs:
Organic-walled microfossils common throughout the Proterozoic
and early Paleozoic

adaptation:
Any heritable characteristic of an organism that improves
its ability to survive and reproduce in its environment. Also
used to describe the process of genetic change within a population,
as influenced by natural selection. Alternatively, some heritable
feature of an individual's phenotype that improves its chances
of survival and reproduction in the existing environment.

adaptive
radiation (also "radiation", for short): The diversification,
over evolutionary time, of a species or group of species into
several different species or subspecies that are typically
adapted to different ecological niches (for example, Darwin's
finches). The term can also be applied to larger groups of
organisms, as in "the adaptive radiation of mammals."
For example, trilobites underwent a massive radiation during
the Cambrian, and insects during the Cretaceous.

agnathans:
A jawless, heavily armored fish that appeared in the Devonian.

algae:
Photosynthetic, almost exclusively aquatic, nonvascular plant-like
organisms that appeared in the Precambrian and that range
in size from simple unicellular forms to giant kelps.

allele:
One of the alternative forms of a gene. For example, if a
gene determines the color of eyes, one allele of that gene
may produce brown eyes and another allele produce blue eyes.
In a diploid cell there are usually two alleles of any one
gene (one from each parent). Within a population there may
be many different alleles of a gene; each has a unique nucleotide
sequence.

allopatric
speciation: Speciation
that occurs when two or more populations of a species are
geographically isolated from one another sufficiently that
they do not interbreed.

allopatry:
Living in separate places. Compare with sympatry.

allotype:
specimen designated from the type series that is the opposite
sex of the holotype.

amino
acid: The unit molecular building
block of proteins, which are chains of amino acids in a certain
sequence. There are 20 main amino acids in the proteins of
living things, and the properties of a protein are determined
by its particular amino acid sequence.

amino
acid sequence: A series of
amino acids, the building blocks
of proteins, usually coded for by DNA. Exceptions are those
coded for by the RNA of certain viruses, such as HIV.

ammonoids:
Cephlapods that evolved from nautiloids
and are generally spiral-shaped shell with numerous chambers.

amphibians:
A transitional group of vertebrates between fish and reptiles,
capable of living on land, but returning to the water to reproduce.
( lived from Devonian to Holocene).

apomorph:
an evolutionarily advance in character state. The long neck
of the giraffe is apomorphic; the short neck of its ancestor
is plesiomorphic. In cladistics, a character state that is
present throughout a clade but is not present in any close
outgroup of the clade.

archaeans:
single-celled creatures that along with eubacteria
(true bacteria) make up a category of life called the prokaryotes.
While archaeans resemble bacteria and have some genes that
are similar to bacterial genes, they also contain other genes
that are more like what you'd find in eukaryotes.
Furthermore, they have some genes that aren't like any found
in any other organism, which is why they have been now distinguished
by their own third domain of life.

Archaeocyaths:
conical, calcareous, Cambrian fossils with a long history
of phylogenetic uncertainty and
changing interpretations. There is now a strong consensus
that archaeocyaths are sponges.

arthropod:
an invertebrate having jointed limbs and a segmented body
with an exoskeleton made of chitin

ATP
or adenosine triphosphate: a relatively stable, energy-dense
molecule broken down in cells to obtain energy.

bedding
plane: A surface separating layers of sedimentary rocks and
deposits. A bedding plane marks termination of one deposit
and beginning of another of different character, such as a
surface separating a sandstone bed from an overlying mudstone
bed. Rocks tend to breaks or separate along bedding planes.

benthic:
term used to designate aquatic organisms that are bottom dwelling.

bilateral
symmetry: The condition, found
in many organisms, where one half of the body or structure
is the mirror image of the other.

bilaterians:
A clade of animals whode members share: bilateral
symmetry, are triploblastic (three tissue layers: ectoderm,
mesoderm, endoderm), and with HOX genes in one or more clusters
with the genes within a cluster arranged in the same order
as the body parts they affect.

biological
species concept: The
concept of species, according to which a species is a set
of organisms that can interbreed among each other. Compare
with cladistic species concept, ecological species concept,
phenetic species concept, and recognition species concept.

biostatigraphy:
The branch of geology concerned with the separation and differentiation
of rock units by means of the study of the fossils they contain.

bioturbation:
disturbance of sediment layers due to biological activity.
This is a significant process in the marine environment where
many animals such as worms exist by consuming organic matter
trapped between sediment grains. Animals like clams burrow
through sediment to hide from predators swimming or crawling
above the ocean floor. The activity of the animals sedimentary
features.

bivalve:
A mollusk having two shells hinged together, as the oyster,
clam, or mussel; or any animal with two halves to its shell
such as an ostracode or brachiopod.

bolide:
very generally, an extraterrestrial body of indeterminant
composition, in the 1-10-km size range, that impacts the earth
at velocities faster than a bullet (20-70 km/sec = Mach 75),
explodes upon impact, and creates a large crater.
bony fishes: Fish of the class Osteichthyes, characterized
by a skeleton composed of bone in addition to cartilage, gill
covers, and an air bladder.

brachiopods:
A group of clam-like marine invertebrates separated into the
Articulata and the Inarticulata based on shell morphology.
(Cambrian to Recent)

breccia:
a rock formed similarly to conglomerate,
except that breccia's rock fragments are very sharp and angular.
These irregular rock fragments have not been transported by
water, wind, or glaciers long enough to be rounded and smoothed
as in conglomerate. The cementing agents silica, calcite
(CaCO3), and iron oxides are the same as in conglomerate.

bryophyta:
Bryophytes comprise the mosses (Class Musci), as well as liverworts
(Class Hepaticae) and hornworts (Class Anthocerotae). They
are believed to have been the first true plants, evolving
from charophytes almost 500 million years ago. Unlike other
plants, bryophytes do not have true organs, such as leaves,
stems, or roots. In place of roots, most bryophytes have thin,
hairy tubes called rhizoids that provide anchorage and nutrient
uptake from the soil. The bryophyte life cycle is unique in
having a dominant gametophyte generation. The actual green
plant in mosses and worts is the gametophyte plant, while
the sporophyte consists of simply an enclosed sporangium,
typically atop a stalk.

calcareous:
Of, containing, or like calcite (calcium carbonate).

calcite:
A common compound (CaCO3) in rock formation and the main component
of limestone. Calcite can be many colors and effervesces (bubbles)
in hydrochloric acid.

Camerate
crinoids: crinoids where the calyx has a rigid union of all
plates. In the older varieties, the plates of the calyx are
small; also in older varieties, the arms are composed of plates
that are nearly equal in size.

carbonate
rock: A rock consisting primarily
of a carbonate mineral such as calcite or dolomite, the chief
minerals in limestone and dolostone, respectively.

carpoids
(formally Homalozoa): Extinct subphylum (Phylum Enchinodermata)
whose members have no trace of radial
symmetry. The theca is depressed and asymmetrical. Homalozoa
are known from Middle Cambrian to Middle Devonian rocks.

catabolism:
the destructive metabolism of larger organic molecules into
smaller constituents, usually with the release of energy (usually
as ATP).

cephalopod
- A group of mollusks resembling an octopus or squid usually
with a chambered shell. This shell can be straight or coiled.

chalk:
A variety of limestone made up in part of biochemically derived
calcite, in form of skeletons or skeletal fragments of microscopic
oceanic plants and animals mixed with fine-grained calcite
deposits of biochemical or inorganic-chemical origin.

chert:
A cryptocrystalline form of quartz, microscopically granular.
Occurs as nodules and as thin, continuous layers. Duller,
less waxy luster than chalcedony. Occurs in limestone, dolostone,
and mudstones. It may form from deposition and compaction
of silica-rich skeletons of diatoms, radiolarians (a common
ocean planktonic animal), and
tiny sponge fragments called spicules. Being composed of silica,
chert is very hard and durable. Flint is a very dark form
of chert.

chromosome:
A structure in the cell nucleus that carries DNA.
At certain times in the cell cycle, chromosomes are visible
as string-like entities. Chromosomes consist of the DNA with
various proteins, particularly histones, bound to it.

chitin:
carbohydrate polymer found in the cell walls of fungi and
in the exoskeletons of arthropods
that provides strength for support and protection.

clade:
A set of species descended from a common
ancestral species. Synonym of monophyletic group.

cladism:
Phylogenetic classification. The members of a group in a cladistic
classification share a more recent common ancestor with one
another than with the members of any other group. A group
at any level in the classificatory hierarchy, such as a family,
is formed by combining a subgroup at the next lowest level
(the genus, in this case) with
the subgroup or subgroups with which it shares its most recent
common ancestor. Compare with evolutionary classification
and phenetic classification.

cladistic
species concept: The
concept of species, according to which a species is a lineage
of populations between two phylogenetic branch points (or
speciation events). Compare with biological species concept,
ecological species concept, phenetic species concept, and
recognition species concept.

cladogram:
A branching diagram that illustrates hypotheses about the
evolutionary relationships among groups of organisms. Cladograms
can be considered as a special type of phylogenetic tree that
concentrates on the order in which different groups branched
off from their common ancestors. A cladogram branches like
a family tree, with the most closely related species on adjacent
branches.

clastic:
Refers to rock or sediments made up primarily of broken fragments
of pre-existing rocks or minerals.

coccoliths:
Microscopic structures of varying shape and size that are
made of calcite, are secreted by calcareous nannoplankton,
and are found in marine deposits from the Triassic period
to the Recent. Coccoliths range in size from one to thirty-five
microns.

codon:
A triplet of bases (or nucleotides) in the DNA
coding for one amino acid. The relation between codons and
amino acids is given by the genetic code. The triplet of bases
that is complementary to a condon is called an

anticodon;
conventionally, the triplet in the mRNA is called the codon
and the triplet in the tRNA is called the anticodon.

coelom:
body cavity within which internal organs can develop, which
is completely lined with tissue of mesodermal origin.

concretion:
A compact mass of mineral matter, usually spherical or disk-like
in shape and embedded in a host rock of different composition.
They form by precipitation of mineral matter about a nucleus
such as a leaf, trilobite exoskelton or a piece of shell of
bone.

conglomerate:
a clastic sedimentary rock that forms from the cementing of
rounded cobble and pebble sized rock fragments. Conglomerate
is formed by river movement or ocean wave action. The cementing
agents that fill the spaces to form the solid rock conglomerate
are silica, calcite, or iron oxides.

continental
crust: Solid, outer layers of the earth, including the rocks
of the continents. The part of the crust that directly underlies
the continents and continental shelves. Averages about 35
km in thickness, but may be over 70 km thick under largest
mountain ranges.

continental
drift: The theory that horizontal movement of the earth's
surface causes slow, relative movements of the continents
toward or away from one another.

continental
shelf: That portion of the continental margin that extends
as a gently sloping surface from theshoreline seaward to a
marked change in slope at the top of the continental slope
. Seaward depth averages about 130 m.
continental slope: That portion of the continental margin
that lies between the continental shelf and the continental
rise. It is relatively steep, i.e., 3o - 6o degrees. The continental
slope is underlain by crustal rocks of the continent.

continental
rise: That portion of the continental margin that lies between
the abyssal plain and the continental slope. The continental
rise is underlain by crustal rocks of the ocean basin.

coprolite:The
fossilized waste (dung; fecies) matter of animals.
craton: A part of the earth's crust that has attained stability
and has been little deformed for a prolonged period.

cytoplasm:
The region of a eukaryotic cell outside the nucleus.

cyanobacteria:
general term for a large group of photosynthetic Eubacteria
still often called "blue-green algae", though they
are Eubacteria, and not algaea. The name derives from their
use of phycocyanin (a bluish pigment), as well as chlorophyll
a (a green pigment), for the photosynthesis
of carbohydrates.They are widespread in aquatic environments
including oceans, ponds, lakes, tidal flats, and moist soil.
Cyanobacteria exist mostly as colonies and filaments and sometimes
as single cells. Filamentous forms such as Oscillatoria sp.
rotate in a screwlike manner for locomation, while the gelatinous
forms glide along in a mucus-like slime they produce. Blue-green
algae produce gelatinous capsules which are often lighter
than water floatotion to keep them near the surface of the
water where there is the most sunlight. Reproduction in the
cyanobacteria is by fission. The cells of the cyanobacteria
reveal a considerable level of complexity. Their chlorophyll
is integrated into thylakoids, extensions of the cell membrane.
Actually, the entire photosynthetic cell is comparable to
a eukaryotic chloroplast. Photosynthesis
in the cyanobacteria is nearly identical, biochemically, to
that of the algae and the green plants. Like the algae and
plants, their photosynthetic pigments include chlorophyll
a and the accessory pigment beta carotene, although they lack
chlorophyll b. The glucose produced by the cyanobacteria photosynthesis
is stored in their own form of starch, which is similar to
animal glycogen.

Darwinian
evolution: Evolution by the process of natural
selection acting on random variation.

Deuterostome:
Clade of bilateran animals
that share multiple HOX genes for
the posterior. Means "second mouth", so called because
the mouth develops from the second opening into the embryonic
gut. The first opening (the blastopore) forms the future anus
only, and the mouth forms later. The body cavity (coelom)
develops from buds off the gut.

diagenesis:
The physical, chemical or biological alteration of sediments
into sedimentary rock at relatively
low temperatures and pressures that can result in changes
to the rock's original mineralogy and texture. After deposition,
sediments are compacted as they are buried beneath successive
layers of sediment and cemented by minerals that precipitate
from solution. Grains of sediment, rock fragments and fossils
can be replaced by other minerals during diagenesis. Porosity
usually decreases during diagenesis, except in rare cases
such as dissolution of minerals and dolomitization.

diploid:
Having two sets of genes and two sets of chromosomes (one
from the mother, one from the father). Many common species,
including humans, are diploid. Compare with haploid and polyploid.

diversity
(or genetic diversity): A measure of the possible choices
of different information at a gene. For example, whether it
codes for brown or blue eyes.

DNA:
Anucleic acid that constitutes the genetic material of all
cellular organisms and the DNA viruses; DNA replicates and
controls through messenger RNA the inheritable characteristics
of all organisms. A molecule of DNA is made up of two parallel
twisted chains of alternating units of phosphoric acid and
deoxyribose, linked by crosspieces of the purine bases and
the pyrimidine bases, resulting in a right-handed helical
structure, that carries genetic information encoded in the
sequence of the bases. Also, DEOXYRIBONUCLEIC ACID.

dolomite:
A class of carbonate sedimentary rock. Called dolomite or
dolomitic limestone, it is uncertain how dolomite beds formed
since it does not form on the surface of the earth in modern
times, yet massive layers of dolomite can be found in ancient
rocks. It is conjectured this is because it undergoes a significant
mineralogical change after deposition. Originally deposited
as calcite or aragonite rich limestones, it subsequently undergoes
a process called diagenesis where the calcite and/or aragonite
is altered to dolomite

dominance
(genetic): An allele (A) is dominant
if the phenotype of the heterozygote (Aa) is the same as the
homozygote (AA). The allele (a) does not influence the heterozygote's
phenotype and is called recessive. An allele may be partly,
rather than fully, dominant; in that case, the heterozygous
phenotype is nearer to, rather than identical with, the homozygote
of the dominant allele.

Dorsal
- The back side of the body of a vertebrate (opposite of ventral).

ecological
species concept: A
concept of species, according to which a species is a set
of organisms adapted to a particular, discrete set of resources
(or "niche") in the environment. Compare with biological
species concept, cladistic species concept, phenetic species
concept, and recognition species concept.

endosymbiosis:
The relationship between organisms which live one within another
(symbiont within host) in a mutually beneficial relationship.
This process is believed to have accurred in the the evolution
of eukaryotes from prokaryotes
involved the symbiotic union of several previously independent
ancestors. According to the theory, these ancestors included
a host cell, an ancestor of mitochondria, an ancestor of chloroplasts,
and, more controversially, a prokaryote that brought with
it the structures that today provide cellular motion.

environmental
variance: Within a population,
the measure of how much of the variation of a particular phenotype
is due to environmental factors (as opposed to variations
in genotype - see genetic variance). An example might be the
height of a plant as determined by such factors as nutrition
or damage during development.

enzyme:
a protein that catalizes biochemical reactions; nzymes are
important in the construction and degradation of other molecules.

eubacteria:
the true bacteria, that under the three domain of life system
one of the prokaryotes; the other
are the archaeans.

eukaryote:
Any organism made up of eukaryotic cells with a nuceus containing
DNA and other organelles. Together, eukaryotes comprise one
of the three domains of life. Eukaryotes are generally larger
and have more DNA than prokaryotes whose cells do not have
a nucleus to contain their DNA. Almost
all multicellular organisms are eukaryotes.

eumetazoa:
The primary clade of Kindom Animalia that can be considered
a subkingdom. The cells of Eumetazoans truly co-operate to
form unmistakable tissues and organs. Nutrients and signals
(e.g., hormones) flow efficiently betwwen cells, such that
only specialized cells are involved in the acquisition of
food.

exon:
The nucleotide sequences of some genes
consist of parts that code for amino acids, with other parts
that do not code for amino acids interspersed among them.
The coding parts, which are translated, are called exons;
the interspersed non-coding parts are called introns.

facies,
metamorphic: A set of metamorphic
mineral assemblages, repeatedly associated in space and time,
such that there is a constant and therefore predictable relationship
between mineral composition and chemical composition. That
relationship is a consequence of conditions of temperature
and pressure under which the assemblages are stable.

family:
The category of taxonomic classification between order and
genus (see taxon). Organisms within a
family share a close similarity; for example, the cat family,
Felidae, which includes lions and domestic cats.

fauna:
animals that are characteristic of a certain age, locality,
or formation.

fitness:
The success of an individual (or allele
or genotype in a population) in surviving
and reproducing, measured by that individual's (or allele's
or genotype's) genetic contribution to the next generation
and subsequent generations.

fossil:
the recognizable remains, such as bones, shells, or leaves,
or other evidence, such as tracks, burrows, or impressions,
of past life on earth.

fungi:
A group of organisms comprising the kingdom Fungi within Domain
Eukarya, which includes molds and
mushrooms. They can exist either as single cells or make up
a multicellular body called a mycelium. Fungi lack chlorophyll
and secrete digestive enzymes that decompose other biological
tissues.

gamete:
Haploid reproductive cells that combine at fertilization to
form the zygote, called sperm (or pollen) in males and eggs
in females.

gene:
A sequence of nucleotides coding for a protein (or, in some
cases, part of a protein); a unit of heredity.
gene expression: The degree to which a gene is active in a
certain tissue of the body, measured by the amount of mRNA
in the tissue.

genetic:
Related to genes. A gene is a sequence of nucleotides coding
for a protein (or, in some cases, part of a protein); a unit
of heredity.

genetics:
The study of genes and their relationship to characteristics
of organisms.

genetic
code: The code relating nucleotide triplets in the mRNA (or
DNA) to amino acids in the proteins.

genetic
drift: Changes in the frequencies of alleles in a population
that occur by chance, rather than because of natural selection.

genetic
variance: Within a population, the measure of how much of
the variation of a particular phenotype is due to genotypic
variation (as opposed to environmental factors - see environmental
variance). An example might be the height of a tree as determined
by genes inherited from the parents.

genome:
The full set of DNA in a cell or organism.

Genomics:
The science dealing with analysis of the full range of genes
in an organism.

genotype:
The set of two genes possessed by an individual at a given
locus. More generally, the genetic profile of an individual.

genus
(plural genera): The second-to-lowest category in taxonomic
classification. The phrase "species name" generally
refers to the genus and species together, as in the Latin
name for humans, Homo sapiens. See taxon.

glaciation:
The formation of large sheets of ice across land. Glaciation
of the continents marks the beginning of ice ages, when the
makeup of Earth and organisms on it changes dramatically.

glucose:
a simple sugar that is the primary product of photosynthesis.
It is polymerized to make cellulose and chitin.

Gondwana:
The southern portion of the late Paleozoic supercontinent
known as Pangea. It means, literally "Land of the Gonds"
(a people of the Indian subcontinent).

haploid:
The condition of having only one set of genes or chromosomes.
In normally diploid organisms such as humans, only the gametes
are haploid.

hardness:
The resistance of a mineral to scratching.

heterotrophic:
Comprise organisms that are not self-sustaining; that is,
they derive energy from the oxidation of organic compounds
either by consumption or absorption of other organisms.

heterozygote:
An individual having two different alleles at a genetic locus.
Compare with homozygote.

holotype:
specimen that serves as the standard bearer of a species
or subspecies name.

Homalozoa
(informally carpoids): Extinct subphylum (Phylum Enchinodermata)
whose members have no trace of radial symmetry. The theca
is depressed and asymmetrical. Homalozoa are known from Middle
Cambrian to Middle Devonian rocks.

HOX
genes (Hox cluster): Genes (transcription
factors) paramount in development and found to be highly conserved
in evolution. Occuring in clusters they act as master switches
for other genes in that express and time developmental processes.
The genomes of all animals that have been sequenced have at
least one Hox cluster that show strong homology to the genes
in Drosophila (the friut fly). For example, mice and humans
have 4 Hox clusters (a total of 39 genes in humans) located
on four different chromosomes.

ichnofossils:
trace fossils that are seen as preserved tracks or other signs
of the behaviors of animals in the substrate. Ichnofossils
can provide insights on the behavior of an extinct animal.
Very rarely is the animal itself found in direct association
with the ichnofossil it created.

intron:
The nucleotide sequences of some genes consist of parts that
code for amino acids, and other parts that do not code for
amino acids interspersed among them. The interspersed non-coding
parts, which are not translated, are called introns; the coding
parts are called exons.

Kingdom
Animalia: Comprises the animals.
These are eukaryotic multicellular
organisms with cells that lack a cell wall. Many are capable
of movement, or movement of some of their body parts, at some
time of their life. Animals are heterotrophic, that is, they
cannot obtain energy from non-living forms and must eat other
organisms, or their products, to obtain energy.

Kingdom
Fungi: Comprise mushrooms, yeasts,
and other fungi. These are eukaryotic
multicellular organisms that are typically non-moving, have
a cell surrounded by a cell wall, and are heterotrophic, that
is, they cannot use energy from non-living forms and must
consume other organisms, or their products, to obtain energy.
Many are decomposers, that is, they obtain energy by breaking
down molecules in dead, decaying organisms.

Kingdom
Monera: Comprise bacteria
and cyanobacteria. These are unicellular organisms that are
prokaryotic, that is, do not have
a nucleus surrounded by a nuclear membrane. The bacteria are
mostly heterotrophic, that is,
they cannot obtain energy from non-living forms and must eat
other organisms, or their products, to obtain energy. The
cyanobacteria are autotrophic, that is, they can convert energy
from non-living forms into biologically useful energy (stored
in the chemical bonds of biological molecules); cyanobacteria,
like plants, accomplish this through the process of photosynthesis.

Kingdom
Plantae: Comprise the plants.
These are eukaryotic multicellular
organisms with cells surrounded by a cell wall made of the
carbohydrate cellulose. Plants are typically non-mobile. They
are autotrophic, that is, they
can convert energy from non-living forms into biologically
useful energy (stored in the chemical bonds of biological
molecules); plants accomplish this through the process of
photosynthesis, synthesis of
energy-containing biological compounds by trapping light energy.

Kingdom
Protista: Comprise unicellular organisms
that are eukaryotic, that is, have
a nucleus separated from the cytoplasm of the cell by a nuclear
membrane. Some are plant-like in that they are autotrophic,
while others are animal-like in that they are heterotrophic.

Laurasia:
The northern portion of the late Paleozoic supercontinent
called Pangea.
lithosphere: the outer skin of the earth, composed of the
crust and the uppermost mantle.

limestone:
the most abundant of the non-clastic sedimentary rocks that
is produced from the mineral calcite (calcium carbonate) and
sediment. The main source of limestone is the limy ooze formed
in the ocean. The calcium carbonate can be precipitated from
ocean water or it can be formed from sea creatures that secrete
lime such as algae and coral.

lophotrochozoans:
A clade of animals that share a cluster of HOX genes quite
different from those found in the ecdysozoans (and deuterostomes).
They share similar sequences in their 18S rRNA genes. The
phylogeny of this clade that includes brachiopods, mulluscs,
bryozoa, and many other groups is the subject of many competing
hypothses.

mantle:
The zone of the earth below the crust and above the core.

marl:
marine sediment made of sand, clay, and glauconite in different
ratios.
matrix: The solid matter in which a fossil or crystal is embedded.
Also, a binding substance (e.g., cement in concrete).

messenger
RNA (mRNA): The molecule transcribed by
DNA that then carries genetic information
from a gene to the site in the cell where the information
determines the order of amino acids in the synthesis of a
protein.

metabolism:
the uptake and digestion of food, and the disposal of waste
products in a living organism, including synthesis of organic
molecules (anabolism) and their breakdown (catabolism).
This is to be distinguished from cell metabolism which is
the process of metabolism occuring within a single cell. Cell
metabolism is the process by which individual cells process
nutrient molecules.

metazoa:
subkingdom of the animal kingdom
comprising the multicellular animals in the traditional two-kingdom
system of taxonomic classification, in which living organisms
were considered to be either plants or animals.

mineralization:
replacement of organic or inorganic matter by minerals such
as silica, calcite or iron during the process of fossilization.

monophyletic:
A group composed of a collection of organisms, including the
most recent common ancestor of all those organisms and all
the descendants of that most recent common ancestor. A monophyletic
taxon is also called a clade.

morphology:
study of form and structure of animals and plants and their
fossil remains.

mycetozoa:
a group of eukaryotic organisms reproducing
themselves by spores. These are produced in or on sporangia
which are formed in the air and the spores are distributed
by the currents of air. They thus differ from other spore-bearing
members of the animal kingdom (which produce their spores
while immersed in water or, in the case of parasites, within
the fluids of their hosts), and resemble the Fungi
and many of the lower green plants.

natural
selection: The differential
survival and reproduction of classes of organisms that differ
from one another in on or more usually heritable characteristics.
Through this process, the forms of organisms in a population
that are best adapted to their local environment increase
in frequency relative to less well-adapted forms over a number
of generations. This difference in survival and reproduction
is not due to chance.
organism: Any individual living thing.

oncolite:
small, often spheroidal, concentrically laminated, calcium-carbonate
sedimentary structure or stromatolite that may form in highly
saline (salty) waters.

organism:
individual member of a species, that is, a single biological
entity.

ostraderms:
Primitive jawless fishes, covered by bony armor, that lived
in the Cambrian through Devonian periods.

oxidation:
The act of oxidizing or state of being oxidized. Chemically
it consists in the increase of positive charges on an atom
or the loss of negative charges. Most biological oxidations
are accomplished by the removal of a pair of hydrogen atoms
(dehydrogenation) from a molecule. Such oxidations must be
accompanied by reduction of an acceptor molecule.

pelagic:
Refers to fish and animals that live in the open marine environment,
away from the sea bottom.

paleobiology:
The biological study of fossils.

paleomagnetism:
Study of the Earth's past magnetism as it is recorded in the
rocks.

paleontologist:
A scientist who studies fossils to better understand life
in prehistoric times.

Pangea:
A supercontinent that existed from about 300 to 200 million
years ago, and included most of the continental crust of the
Earth.

parallelism:
an evolutionary pattern that results in the formation of homologous
character states when their exists a common ancestor.

parapatric
speciation: Speciation
in which the new species forms from a population contiguous
with the ancestral species' geographic range.

paraphyletic
group: A set of species containing
an ancestral species together with some, but not all, of its
descendants. The species included in the group are those that
have continued to resemble the ancestor; the excluded species
have evolved rapidly and no longer resemble their ancestor.

paratype:
All of the specimens in the type series of a species
or subspecies other than the holotype.

peripatric
speciation: A synonym of
peripheral isolate speciation.

peripheral
isolate speciation:
A form of allopatric speciation
in which the new species is formed from a small population
isolated at the edge of the ancestral population's geographic
range. Also called peripatric
speciation.

Pharmacogenomics:
The application of genomic information to clinical trials
to determine which patients, based on their genetic make-up,
are most likely to benefit from a certain drug or which are
likely to suffer adverse effects.

photosynthesis:
The fundamental biological process by which green plants make
organic compounds such as carbohydrates from atmospheric carbon
dioxide and water using light energy from the Sun. The process
has two main phases: the light-dependent light reaction responsible
for the initial capture of energy, and the light-independent
dark reaction in which this energy is stored in the chemical
bonds of organic molecules. Since virtually all other forms
of life are directly or indirectly dependent on green plants
for food, photosynthesis is the basis for almost all life
on earth.

phycocyanin:
a blue water soluble pigment used in cyanobacteria and the
red algae to absorb sunlight in photosynthesis.

phycoerythrin:
a red, water-soluble pigment found used in cyanobacteria and
red algae to absorb sunlight in photosynthesis.

phylogeny:
The study of ancestral relations among species, often illustrated
with a "tree of life" branching diagram, which is
also known as a phylogenetic tree.

phylum
(plural phyla): One of the highest levels of taxonomic classification.
See taxon.

physiological
pathway (or simply pathway): The sequence of biochemical interactions
among proteins that regulates the function of living cells.

phytoplankton:
Microscopic aquatic organisms that, like plants, use photosynthesis
to capture and harness solar energy; term is primarily used
in ecology.

polygenetic:
Originating in various ways or from various sources.

plate
tectonics: The theory that the
surface of the earth is made of a number of plates, which
have moved throughout geological time resulting in the present-day
positions of the continents. Plate tectonics explains the
locations of mountain building as well as earthquakes and
volcanoes. The rigid plates consist of continental and oceanic
crust together with the upper mantle, which "float"
on the semi-molten layer of the mantle beneath them, and move
relative to each other across the earth. Six major plates
(Eurasian, American, African, Pacific, Indian, and Antarctic)
are recognized, together with a number of smaller ones. The
plate margins coincide with zones of seismic and volcanic
activity.

polymorphism:
A condition in which a population possesses more than one
allele at a locus. Sometimes it is defined
as the condition of having more than one allele with a frequency
of more than five percent in the population.

polyphyletic
group: A set of species descended
from more than one common ancestor. The ultimate common ancestor
of all species in the group is not a member of the polyphyletic
group, usually because the common ancestor lacks the characteristics
of the group.

polyploid:
An individual containing more than two sets of genes
and chromosomes.

population:
A group of organisms, usually a group of sexual organisms
that interbreed and share a gene pool, and are normally relatively
isolated from other groups of the same species.

postzygotic
isolation: A form of reproductive
isolation in which a zygote is successfully
formed but then either fails to develop or develops into a
sterile adult. Donkeys and horses are postzygotically isolated
from one another; a male donkey and a female horse can mate
to produce a mule, but the mule is sterile.

prezygotic
isolation: A form of reproductive
isolation in which the two species never reach the stage of
successful mating, and thus no zygote is formed. Examples
would be species that have different breeding seasons or courtship
displays, and which therefore never recognize one another
as potential mates.

probe
array: Used in microarray technology
- a silicon or glass chip to which small pieces of DNA, or
probes, have been attached, with each probe representing a
sequence of bases unique to a known gene or gene fragment.
Also known as a microarray or DNA chip.

prokaryote:
A cell without a distinct nucleus. Bacteria and some other
simple organisms are prokaryotic. Compare with eukaryote.
All prokaryotes form a paraphyletic grouping.

protaspis:
The earliest stage recognized in larval trilobite (Trilobita)
development. The larva is small, often spiny, and grows through
successive moult stages. Initially it is a small disc but
size and segmentation increase with each successive moult.

protein:
A molecule made up of a sequence of amino acids (there are
23 different amino acids). Many of the important molecules
in a living thing -- for example, all enzymes -- are proteins.

protist:
An organism that belongs to the Kingdom
Protista, which includes forms with both plant and animal
affinities, i.e., protozoans, bacteria, and some algae,
fungi, and viruses.

Pterosauria:
meaning "winged lizards" are a clade
of animals partly distinguished by a greatly elongated fourth
digit that supported a membranous wing. They first appeared
in the latter third of the Triassic and survived until the
end of the Cretaceous. Pterosaurs were not dinosaurs, but
were closely related to both dinosaurs and crocodiles.

radial
symmetry: The arrangement of
parts in an organ or organism such that cutting through the
centre of the structure in any direction produces two halves
that are mirror images of each other. The stems and roots
of plants usually show radial symmetry, while all animals
belonging to the Cnidaria (e.g. jellyfish) and Echinodermata
(e.g. starfish) are radially symmetrical - and typically sessile
- in their adult form. The term actinomorphy is used to describe
radial symmetry in flowers.

receptors:
proteins that can bind to other specific
molecules. Usually on the surface of a cell, receptors often
bind to antibodies or hormones.

recessive:
An allele (A) is recessive if the phenotype
of the heterozygote (Aa) is the
same as the homozygote (aa) for the alternative allele (a)
and different from the homozygote for the recessive (AA).
The allele (a) controls the heterozygote's phenotype and is
called dominant. An allele may be partly, rather than fully,
recessive; in that case, the heterozygous phenotype is nearer
to, rather than identical with, the homozygote for the dominant
allele.

recurrent
fauna: A group of animal species
that is found in a particular environment. As the environment
recurs, so does the fauna.

reproductive
isolation: Two populations
or individuals of opposite sex are considered reproductively
isolated from one another if they cannot together produce
fertile offspring. See prezygotic isolation and postzygotic
isolation.

ridge,
oceanic: A major submarine mountain range.

rift
system: The oceanic ridges formed where tectonic plates are
separating and a new crust is being created; also, their on-land
counterparts such as the East African Rift.

rift
zone: A zone of volcanic features associated with underlying
dikes. The location of the rift is marked by cracks, faults,
and vents.

Ring-of-Fire:
The regions of mountain-building earthquakes and volcanoes
which surround the Pacific Ocean.

RNA:
a linear, usually single-stranded polymer of ribonucleotides,
each containing the sugar ribose in association with a phosphate
group and one of four nitrogenous bases: adenine, guanine,
cytosine, or uracil. RNA is found in all living cells; in
prokaryotic and eukaryotic
cells, it encodes the information needed to synthesize proteins
(i.e., it copies "instructions" that it receives
from DNA); in certain viruses, it serves as the genome. (An
abbreviation for ribonucleic acid.)

sandstone:
A clastic sedimentary rock in which the particles are dominantly
of sand size, from 0.062 mm to 2 mm in diameter. Quartz is
the most abundant mineral that forms sandstone.

sclerotin:
an insoluble tanned protein permeating and stiffening the
chitin of the cuticle of arthropods

seafloor
spreading: The mechanism by which new seafloor crust is created
at oceanic ridges and slowly spreads away as plates are separating.

seamount:
A submarine volcano.

sedimentary
facies: An accumulation of deposits that exhibits specific
characteristics and grades laterally into other sedimentary
accumulations that were formed at the same time but exhibit
different characteristics.

sedimentary
rock: Rock formed from the accumulation
of sediment, which may consist of fragments and mineral grains
of varying sizes from pre-existing rocks, remains or products
of animals and plants, the products of chemical action, or
mixtures of these.

sequence
or nucleotide sequence: The order of the chemical bases -adenine
(A), thymine (T), cytosine (C), and guanine (G)-in a gene.
The base sequence determines the order of amino acids making
up the protein encoded by the gene.

shale:
A mudstone that easily splits or fractures.

silica:
A chemical combination of silicon and oxygen. It is a structural
component in many organisms, such as diatoms.

Single
nucleotide polymorphism
(SNP): A site on the DNA at which the base
sequence differs among individuals. (The abbreviation is pronounced
"snip.")

speciation:
Changes in related organisms to the point where they are different
enough to be considered separate species. This occurs when
populations of one species are separated and adapt to their
new environment or conditions (physiological, geographic,
or behavioral).

synapomorph:
apomorphic features that two or more taxa
have in common. If the two groups share a character state
that is not the primitive state, they may be related in an
evolutionary context, and only synapomorph character states
can be used as evidence that taxa are related. Phylogenic
trees are built up by discovering groups united by synapomorphies.
In cladistics, an apomorphy occurs in two related clades and
thereby supports grouping of the two clades into a single
larger clade.

synapomorphy:
a morphologic character derived in order to infer common ancestry
among taxa under consideration.

taxon
(plural taxa): Any named taxonomic group, such as the family
Felidae, or the genus Homo, or the species sapien. Also see
the tree of life section.

taxonomy:
The theory and practice of biological classification.

trait:
An attribute or character of an individual within a species
for which heritable differences can be defined.

transcription:
The process by which messenger RNA is read from the DNA forming
a gene.

transcriptome:
set of activated genes associated with specific tissue, which
will vary over time.

transfer
RNA (tRNA): A type of RNA that brings
the amino acids to the ribosomes to make proteins. There are
20 kinds of transfer RNA molecules, one
for each of the 20 main amino acids.
A transfer RNA molecule has an amino acid attached to it,
and contains the anticodon corresponding to that amino acid
in another part of its structure. In protein synthesis, each
codon in the messenger RNA combines with
the appropriate tRNA's anticodon, and the amino acids are
arranged in order to make the protein.

vertebrates:
The group (specifically, a subphylum) of animals, descended
from a common ancestor, that share the derived character of
an internal skeleton made of bone or cartilage.

viscosity:
A measure of resistance to flow in a liquid (water has low
viscosity while honey has a higher viscosity.)

zygote:
The cell formed by the fertilization of male and female gametes.